Fix packaging: ship the full backend tree (0.1.0:46)

The image COPY'd backend/server.py + a few subdirs but missed core_migrations.py,
backend/migrations/, and the Phase-1 modules (thesis_review/entity_merge/
entity_jobs). On the box the migrations never ran (tables absent) and those
endpoints 503'd ("Jobs unavailable"). Now COPY backend wholesale (.dockerignore
keeps __pycache__/data out). Bump to 0.1.0:46.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

start9/0.4/Dockerfile

@@ -52,14 +52,13 @@ RUN pip install --no-cache-dir \
       mcp==1.2.0
 
 # ── Application source ──────────────────────────────────────────
-COPY backend/server.py        /app/backend/server.py
-COPY backend/email_integration /app/backend/email_integration
-# Phase-0 substrate: ingest pipeline (entity resolution + backfill) and the
-# CRM MCP server. Shipped alongside the web server so the one-time index build
-# and the (manually-run) MCP server can execute on the box where /data/crm.db
-# lives. See start9/0.4/INGEST_PACKAGING.md.
-COPY backend/ingest           /app/backend/ingest
-COPY backend/mcp              /app/backend/mcp
+# Whole backend tree: server.py + all top-level modules (core_migrations,
+# thesis_review, entity_merge, entity_jobs) + migrations/ + ingest/ + mcp/ +
+# email_integration/. Earlier piecemeal COPYs missed core_migrations.py, the
+# migrations/ dir, and the Phase-1 modules — so the schema migrations never ran
+# and the thesis / index-job endpoints 503'd ("Jobs unavailable") on the box.
+# .dockerignore keeps __pycache__ and data/ out of the context.
+COPY backend                  /app/backend
 COPY frontend                 /app/frontend
 
 # ── StartOS wrapper scripts ─────────────────────────────────────